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Hoekzema M, Jiang J, Driessen AJM. Optimizing Archaeal Lipid Biosynthesis in Escherichia coli. ACS Synth Biol 2024; 13:2470-2479. [PMID: 39096298 DOI: 10.1021/acssynbio.4c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Membrane lipid chemistry is remarkably different in archaea compared with bacteria and eukaryotes. In the evolutionary context, this is also termed the lipid divide and is reflected by distinct biosynthetic pathways. Contemporary organisms have almost without exception only one type of membrane lipid. During early membrane evolution, mixed membrane stages likely occurred, and it was hypothesized that the instability of such mixtures was the driving force for the lipid divide. To examine the compatibility between archaeal and bacterial lipids, the bacterium Escherichia coli has been engineered to contain both types of lipids with varying success. Only limited production of archaeal lipid archaetidylethanolamine was achieved. Here, we substantially increased its production in E. coli by overexpression of an archaeal phosphatidylserine synthase needed for ethanolamine headgroup attachment. Furthermore, we introduced a synthetic isoprenoid utilization pathway to increase the supply of isopentenyl-diphosphate and dimethylallyl diphosphate. This improved archaeal lipid production substantially. The archaeal phospholipids also served as a substrate for the E. coli cardiolipin synthase, resulting in archaeal and novel hybrid archaeal/bacterial cardiolipin species not seen in living organisms before. Growth of the E. coli strain with the mixed membrane shows an enhanced sensitivity to the inhibitor of fatty acid biosynthesis, cerulenin, indicating a critical dependence of the engineered E. coli strain on its native phospholipids.
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Affiliation(s)
- Mirthe Hoekzema
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, Netherlands
| | - Jiayi Jiang
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, Netherlands
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2
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Jiang Z, Chen JA, Mohamed OG, Huynh J, Chen A, Tripathi A, La Clair JJ, Burkart MD. Cryptic Cerulenin Rearrangement in Ketosynthase Covalent Inhibition. J Am Chem Soc 2024; 146:20370-20378. [PMID: 38981108 DOI: 10.1021/jacs.4c05938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The antibiotic cerulenin is a fungal natural product identified as a covalent inhibitor of ketosynthases within fatty acid and polyketide biosynthesis. Due to its selective and potent inhibitory activity, cerulenin has found significant utility in multidisciplinary biochemical, biomedical, and clinical studies. Although its covalent inhibition profile has been confirmed, cerulenin's mechanism has not been fully determined at a molecular level, frustrating the drug development of related analogues. Herein, we describe the use of stable isotopic tracking with NMR and MS methods to unravel the covalent mechanism of cerulenin against type II fatty acid ketosynthases. We detail the discovery of a unique C2-C3 retro-aldol bond cleavage and a structural rearrangement upon covalent inhibition of cerulenin at the active cysteine residue in E. coli type II fatty acid ketosynthases FabB and FabF.
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Affiliation(s)
- Ziran Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Jeffrey A Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Osama G Mohamed
- Natural product Discovery Core - Life Sciences Institute, University of Michigan, Mary Sue Coleman Hall, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Kasr el Aini Street, Cairo 11562, Egypt
| | - Jennifer Huynh
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Ashootosh Tripathi
- Natural product Discovery Core - Life Sciences Institute, University of Michigan, Mary Sue Coleman Hall, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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3
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Huang H, Chang S, Cui T, Huang M, Qu J, Zhang H, Lu T, Zhang X, Zhou C, Feng Y. An inhibitory mechanism of AasS, an exogenous fatty acid scavenger: Implications for re-sensitization of FAS II antimicrobials. PLoS Pathog 2024; 20:e1012376. [PMID: 39008531 PMCID: PMC11271967 DOI: 10.1371/journal.ppat.1012376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/25/2024] [Accepted: 06/26/2024] [Indexed: 07/17/2024] Open
Abstract
Antimicrobial resistance is an ongoing "one health" challenge of global concern. The acyl-ACP synthetase (termed AasS) of the zoonotic pathogen Vibrio harveyi recycles exogenous fatty acid (eFA), bypassing the requirement of type II fatty acid synthesis (FAS II), a druggable pathway. A growing body of bacterial AasS-type isoenzymes compromises the clinical efficacy of FAS II-directed antimicrobials, like cerulenin. Very recently, an acyl adenylate mimic, C10-AMS, was proposed as a lead compound against AasS activity. However, the underlying mechanism remains poorly understood. Here we present two high-resolution cryo-EM structures of AasS liganded with C10-AMS inhibitor (2.33 Å) and C10-AMP intermediate (2.19 Å) in addition to its apo form (2.53 Å). Apart from our measurements for C10-AMS' Ki value of around 0.6 μM, structural and functional analyses explained how this inhibitor interacts with AasS enzyme. Unlike an open state of AasS, ready for C10-AMP formation, a closed conformation is trapped by the C10-AMS inhibitor. Tight binding of C10-AMS blocks fatty acyl substrate entry, and therefore inhibits AasS action. Additionally, this intermediate analog C10-AMS appears to be a mixed-type AasS inhibitor. In summary, our results provide the proof of principle that inhibiting salvage of eFA by AasS reverses the FAS II bypass. This facilitates the development of next-generation anti-bacterial therapeutics, esp. the dual therapy consisting of C10-AMS scaffold derivatives combined with certain FAS II inhibitors.
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Affiliation(s)
- Haomin Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shenghai Chang
- Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Cui
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Man Huang
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiuxin Qu
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Huimin Zhang
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xing Zhang
- Center of Cryo-Electron Microscopy, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun Zhou
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Youjun Feng
- Key Laboratory of Multiple Organ Failure, Ministry of Education; Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
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4
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Grundmann CO, Guzman J, Vilcinskas A, Pupo MT. The insect microbiome is a vast source of bioactive small molecules. Nat Prod Rep 2024; 41:935-967. [PMID: 38411238 DOI: 10.1039/d3np00054k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Covering: September 1964 to June 2023Bacteria and fungi living in symbiosis with insects have been studied over the last sixty years and found to be important sources of bioactive natural products. Not only classic producers of secondary metabolites such as Streptomyces and other members of the phylum Actinobacteria but also numerous bacteria from the phyla Proteobacteria and Firmicutes and an impressive array of fungi (usually pathogenic) serve as the source of a structurally diverse number of small molecules with important biological activities including antimicrobial, cytotoxic, antiparasitic and specific enzyme inhibitors. The insect niche is often the exclusive provider of microbes producing unique types of biologically active compounds such as gerumycins, pederin, dinactin, and formicamycins. However, numerous insects still have not been described taxonomically, and in most cases, the study of their microbiota is completely unexplored. In this review, we present a comprehensive survey of 553 natural products produced by microorganisms isolated from insects by collating and classifying all the data according to the type of compound (rather than the insect or microbial source). The analysis of the correlations among the metadata related to insects, microbial partners, and their produced compounds provides valuable insights into the intricate dynamics between insects and their symbionts as well as the impact of their metabolites on these relationships. Herein, we focus on the chemical structure, biosynthesis, and biological activities of the most relevant compounds.
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Affiliation(s)
| | - Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University, Giessen, Germany
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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5
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Rebhi S, Basharat Z, Wei CR, Lebbal S, Najjaa H, Sadfi-Zouaoui N, Messaoudi A. Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae. PeerJ 2024; 12:e17292. [PMID: 38818453 PMCID: PMC11138523 DOI: 10.7717/peerj.17292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/02/2024] [Indexed: 06/01/2024] Open
Abstract
Background & Objectives American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium Paenibacillus larvae, poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against P. larvae, a causative agent of American foulbrood disease in honey bee. Methods We investigated effective novel drug targets through a comprehensive in silico pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of P. larvae genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora (n > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand. Results Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against P. larvae. Conclusions Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry.
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Affiliation(s)
- Sawsen Rebhi
- Université de Tunis-El Manar, Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Tunis, Tunisia
| | | | - Calvin R. Wei
- Department of Research and Development, Shing Huei Group, Taipei, Taiwan
| | - Salim Lebbal
- University of Khenchela, Department of Agricultural Sciences, Faculty of Nature and Life Sciences, Khenchela, Algeria
| | - Hanen Najjaa
- University of Gabes, Laboratory of Pastoral Ecosystem and Valorization of Spontaneous Plants and Associated Microorganisms, Institute of Arid Lands of Medenine, Medenine, Tunisia
| | - Najla Sadfi-Zouaoui
- Université de Tunis-El Manar, Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Tunis, Tunisia
| | - Abdelmonaem Messaoudi
- Université de Tunis-El Manar, Laboratoire de Mycologie, Pathologies et Biomarqueurs, Département de Biologie, Tunis, Tunisia
- Jendouba University, Higher Institute of Biotechnology of Beja, Beja, Tunisia
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6
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Rutherford J, Avad K, Dureja C, Norseeda K, GC B, Wu C, Sun D, Hevener KE, Hurdle JG. Evaluation of Fusobacterium nucleatum Enoyl-ACP Reductase (FabK) as a Narrow-Spectrum Drug Target. ACS Infect Dis 2024; 10:1612-1623. [PMID: 38597503 PMCID: PMC11091888 DOI: 10.1021/acsinfecdis.3c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Fusobacterium nucleatum, a pathobiont inhabiting the oral cavity, contributes to opportunistic diseases, such as periodontal diseases and gastrointestinal cancers, which involve microbiota imbalance. Broad-spectrum antimicrobial agents, while effective against F. nucleatum infections, can exacerbate dysbiosis. This necessitates the discovery of more targeted narrow-spectrum antimicrobial agents. We therefore investigated the potential for the fusobacterial enoyl-ACP reductase II (ENR II) isoenzyme FnFabK (C4N14_ 04250) as a narrow-spectrum drug target. ENRs catalyze the rate-limiting step in the bacterial fatty acid synthesis pathway. Bioinformatics revealed that of the four distinct bacterial ENR isoforms, F. nucleatum specifically encodes FnFabK. Genetic studies revealed that fabK was indispensable for F. nucleatum growth, as the gene could not be deleted, and silencing of its mRNA inhibited growth under the test conditions. Remarkably, exogenous fatty acids failed to rescue growth inhibition caused by the silencing of fabK. Screening of synthetic phenylimidazole analogues of a known FabK inhibitor identified an inhibitor (i.e., 681) of FnFabK enzymatic activity and F. nucleatum growth, with an IC50 of 2.1 μM (1.0 μg/mL) and a MIC of 0.4 μg/mL, respectively. Exogenous fatty acids did not attenuate the activity of 681 against F. nucleatum. Furthermore, FnFabK was confirmed as the intracellular target of 681 based on the overexpression of FnFabK shifting MICs and 681-resistant mutants having amino acid substitutions in FnFabK or mutations in other genetic loci affecting fatty acid biosynthesis. 681 had minimal activity against a range of commensal flora, and it was less active against streptococci in physiologic fatty acids. Taken together, FnFabK is an essential enzyme that is amenable to drug targeting for the discovery and development of narrow-spectrum antimicrobial agents.
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Affiliation(s)
- Jacob
T. Rutherford
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Kristiana Avad
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Chetna Dureja
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
| | - Krissada Norseeda
- Department
of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Bibek GC
- Department
of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Chenggang Wu
- Department
of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Dianqing Sun
- Department
of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawaii at Hilo, Hilo, Hawaii 96720, United States
| | - Kirk E. Hevener
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Julian G. Hurdle
- Center
for Infectious and Inflammatory Diseases, Institute of Biosciences
and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, Houston, Texas 77030, United States
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7
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Jang Y, Lee YJ, Gong G, Lee SM, Um Y, Kim KH, Ko JK. Carbon dioxide valorization into resveratrol via lithoautotrophic fermentation using engineered Cupriavidus necator H16. Microb Cell Fact 2024; 23:122. [PMID: 38678199 PMCID: PMC11055273 DOI: 10.1186/s12934-024-02398-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Industrial biomanufacturing of value-added products using CO2 as a carbon source is considered more sustainable, cost-effective and resource-efficient than using common carbohydrate feedstocks. Cupriavidus necator H16 is a representative H2-oxidizing lithoautotrophic bacterium that can be utilized to valorize CO2 into valuable chemicals and has recently gained much attention as a promising platform host for versatile C1-based biomanufacturing. Since this microbial platform is genetically tractable and has a high-flux carbon storage pathway, it has been engineered to produce a variety of valuable compounds from renewable carbon sources. In this study, the bacterium was engineered to produce resveratrol autotrophically using an artificial phenylpropanoid pathway. RESULTS The heterologous genes involved in the resveratrol biosynthetic pathway-tyrosine ammonia lyase (TAL), 4-coumaroyl CoA ligase (4CL), and stilbene synthase (STS) -were implemented in C. necator H16. The overexpression of acetyl-CoA carboxylase (ACC), disruption of the PHB synthetic pathway, and an increase in the copy number of STS genes enhanced resveratrol production. In particular, the increased copies of VvSTS derived from Vitis vinifera resulted a 2-fold improvement in resveratrol synthesis from fructose. The final engineered CR-5 strain produced 1.9 mg/L of resveratrol from CO2 and tyrosine via lithoautotrophic fermentation. CONCLUSIONS To the best of our knowledge, this study is the first to describe the valorization of CO2 into polyphenolic compounds by engineering a phenylpropanoid pathway using the lithoautotrophic bacterium C. necator H16, demonstrating the potential of this strain a platform for sustainable chemical production.
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Affiliation(s)
- Yongjae Jang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Yeon Ji Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.
- Division of Energy and Environment Technology, KIST School, University of Science and Technology, Seoul, 02792, Republic of Korea.
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8
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Ran X, Parikh P, Abendroth J, Arakaki TL, Clifton MC, Edwards TE, Lorimer DD, Mayclin S, Staker BL, Myler P, McLaughlin KJ. Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis. Acta Crystallogr F Struct Biol Commun 2024; 80:82-91. [PMID: 38656226 PMCID: PMC11058512 DOI: 10.1107/s2053230x2400356x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-acid biosynthesis (Fab) enzymes appealing as drug targets. FabG is an essential FASII enzyme, and some bacteria, such as Mycobacterium tuberculosis, the causative agent of TB, harbor multiple homologs. FabG4 is a conserved, high-molecular-weight FabG (HMwFabG) that was first identified in M. tuberculosis and is distinct from the canonical low-molecular-weight FabG. Here, structural and functional analyses of Mycolicibacterium smegmatis FabG4, the third HMwFabG studied to date, are reported. Crystal structures of NAD+ and apo MsFabG4, along with kinetic analyses, show that MsFabG4 preferentially binds and uses NADH when reducing CoA substrates. As M. smegmatis is often used as a model organism for M. tuberculosis, these studies may aid the development of drugs to treat TB and add to the growing body of research that distinguish HMwFabGs from the archetypal low-molecular-weight FabG.
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Affiliation(s)
- Xinping Ran
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Prashit Parikh
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
| | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | | | - Matthew C. Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Beryllium Discovery Corporation, 7869 Day Road West, Bainbridge Island, WA 98110, USA
| | - Donald D. Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- UCB Pharma, Bedford, Massachusetts, USA
| | | | - Bart L. Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Peter Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), 307 Westlake Avenue North, Seattle, WA 98109, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, Washington, USA
| | - Krystle J. McLaughlin
- Department of Chemistry, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA
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9
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Ali I, Wei DQ, Khan A, Feng Y, Waseem M, Hussain Z, Iqbal A, Ali SS, Mohammad A, Zheng J. Improving the substrate binding of acetyl-CoA carboxylase (AccB) from Streptomyces antibioticus through computational enzyme engineering. Biotechnol Appl Biochem 2024; 71:402-413. [PMID: 38287712 DOI: 10.1002/bab.2548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/15/2023] [Indexed: 01/31/2024]
Abstract
Malonyl-CoA serves as the main building block for the biosynthesis of many important polyketides, as well as fatty acid-derived compounds, such as biofuel. Escherichia coli, Corynebacterium gultamicum, and Saccharomyces cerevisiae have recently been engineered for the biosynthesis of such compounds. However, the developed processes and strains often have insufficient productivity. In the current study, we used enzyme-engineering approach to improve the binding of acetyl-CoA with ACC. We generated different mutations, and the impact was calculated, which reported that three mutations, that is, S343A, T347W, and S350W, significantly improve the substrate binding. Molecular docking investigation revealed an altered binding network compared to the wild type. In mutants, additional interactions stabilize the binding of the inner tail of acetyl-CoA. Using molecular simulation, the stability, compactness, hydrogen bonding, and protein motions were estimated, revealing different dynamic properties owned by the mutants only but not by the wild type. The findings were further validated by using the binding-free energy (BFE) method, which revealed these mutations as favorable substitutions. The total BFE was reported to be -52.66 ± 0.11 kcal/mol for the wild type, -55.87 ± 0.16 kcal/mol for the S343A mutant, -60.52 ± 0.25 kcal/mol for T347W mutant, and -59.64 ± 0.25 kcal/mol for the S350W mutant. This shows that the binding of the substrate is increased due to the induced mutations and strongly corroborates with the docking results. In sum, this study provides information regarding the essential hotspot residues for the substrate binding and can be used for application in industrial processes.
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Affiliation(s)
- Imtiaz Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
- Sunway Microbiome Centre, School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Yuanyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad, Pakistan
| | - Zahid Hussain
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Arshad Iqbal
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Khyber Pakhtunkhwa, Pakistan
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P. R. China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai, P. R. China
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10
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Ghosh T, Barman D, Show K, Lo R, Manna D, Ghosh T, Maiti DK. N-Heterocyclic Carbene-Catalyzed Facile Synthesis of Phthalidyl Sulfonohydrazones: Density Functional Theory Mechanistic Insights and Docking Interactions. ACS OMEGA 2024; 9:11510-11522. [PMID: 38496936 PMCID: PMC10938401 DOI: 10.1021/acsomega.3c08529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 03/19/2024]
Abstract
N-heterocyclic carbene catalysis reaction protocol is disclosed for the synthesis of phthalidyl sulfonohydrazones. A broad range of N-tosyl hydrazones react effectively with phthalaldehyde derivatives under open-air conditions, enabling the formation of a new C-N bond via an oxidative path. The reaction proceeds under mild reaction conditions with broad substrate scopes, wide functional group tolerance, and good to excellent yields. The mechanistic pathway is studied successfully using control experiments, competitive reactions, ESI-MS spectral analyses of the reaction mixture, and computational study by density functional theory. The potential use of one of the phthalidyl sulfonohydrazone derivatives as the inhibitor of β-ketoacyl acyl carrier protein synthase I of Escherichia coli is investigated using molecular docking.
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Affiliation(s)
- Tanmoy Ghosh
- Department
of Chemistry, University of Calcutta, Kolkata 700009, India
| | - Debabrata Barman
- Department
of Chemistry, University of Calcutta, Kolkata 700009, India
| | - Krishanu Show
- Department
of Chemistry, Malda College, Malda, West Bengal 732101, India
| | - Rabindranath Lo
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6, Praha 16610, Czech Republic
| | - Debashree Manna
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, v.v.i., Flemingovo nám. 2, Prague 6, Praha 16610, Czech Republic
- Department
of Applied Chemistry, Maulana Abul Kalam
Azad University of Technology, Haringhata, West Bengal 741249, India
| | - Tapas Ghosh
- Department
of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Dilip K. Maiti
- Department
of Chemistry, University of Calcutta, Kolkata 700009, India
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11
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Guo Q, Zhong C, Dong H, Cronan JE, Wang H. Diversity in fatty acid elongation enzymes: The FabB long-chain β-ketoacyl-ACP synthase I initiates fatty acid synthesis in Pseudomonas putida F1. J Biol Chem 2024; 300:105600. [PMID: 38335573 PMCID: PMC10869286 DOI: 10.1016/j.jbc.2023.105600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 02/12/2024] Open
Abstract
The condensation of acetyl-CoA with malonyl-acyl carrier protein (ACP) by β-ketoacyl-ACP synthase III (KAS III, FabH) and decarboxylation of malonyl-ACP by malonyl-ACP decarboxylase are the two pathways that initiate bacterial fatty acid synthesis (FAS) in Escherichia coli. In addition to these two routes, we report that Pseudomonas putida F1 β-ketoacyl-ACP synthase I (FabB), in addition to playing a key role in fatty acid elongation, also initiates FAS in vivo. We report that although two P. putida F1 fabH genes (PpfabH1 and PpfabH2) both encode functional KAS III enzymes, neither is essential for growth. PpFabH1 is a canonical KAS III similar to E. coli FabH whereas PpFabH2 catalyzes condensation of malonyl-ACP with short- and medium-chain length acyl-CoAs. Since these two KAS III enzymes are not essential for FAS in P. putida F1, we sought the P. putida initiation enzyme and unexpectedly found that it was FabB, the elongation enzyme of the oxygen-independent unsaturated fatty acid pathway. P. putida FabB decarboxylates malonyl-ACP and condenses the acetyl-ACP product with malonyl-ACP for initiation of FAS. These data show that P. putida FabB, unlike the paradigm E. coli FabB, can catalyze the initiation reaction in FAS.
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Affiliation(s)
- Qiaoqiao Guo
- National Key Laboratory of Green Pesticide, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Canyao Zhong
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Huijuan Dong
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Haihong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China.
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12
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Bouymajane A, Filali FR, Moujane S, Majdoub YOE, Otzen P, Channaoui S, Ed-Dra A, Bouddine T, Sellam K, Boughrous AA, Miceli N, Altemimi AB, Cacciola F. Phenolic Compound, Antioxidant, Antibacterial, and In Silico Studies of Extracts from the Aerial Parts of Lactuca saligna L. Molecules 2024; 29:596. [PMID: 38338341 PMCID: PMC10856452 DOI: 10.3390/molecules29030596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Medicinal plants are considered a major source for discovering novel effective drugs. To our knowledge, no studies have reported the chemical composition and biological activities of Moroccan Lactuca saligna extracts. In this context, this study aims to characterize the polyphenolic compounds distributed in hydro-methanolic extracts of L. saligna and evaluate their antioxidant and antibacterial activities; in addition, in silico analysis based on molecular docking and ADMET was performed to predict the antibacterial activity of the identified phenolic compounds. Our results showed the identification of 29 among 30 detected phenolic compounds with an abundance of dicaffeoyltartaric acid, luteolin 7-glucoronide, 3,5-di-O-caffeoylquinic acid, and 5-caffeoylquinic acid with 472.77, 224.30, 196.79, and 171.74 mg/kg of dried extract, respectively. Additionally, antioxidant activity assessed by DPPH scavenging activity, ferric reducing antioxidant power (FRAP) assay, and ferrous ion-chelating (FIC) assay showed interesting antioxidant activity. Moreover, the results showed remarkable antibacterial activity against Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, and Listeria monocytogenes with minimum inhibitory concentrations between 1.30 ± 0.31 and 10.41 ± 0.23 mg/mL. Furthermore, in silico analysis identified three compounds, including Apigenin 7-O-glucuronide, Quercetin-3-O-glucuronide, and 3-p-Coumaroylquinic acid as potent candidates for developing new antibacterial agents with acceptable pharmacokinetic properties. Hence, L. saligna can be considered a source of phytochemical compounds with remarkable activities, while further in vitro and in vivo studies are required to explore the main biological activities of this plant.
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Affiliation(s)
- Aziz Bouymajane
- Biology, Environment and Health Team, Faculty of Sciences and Technologies, Moulay Ismail University, Meknes 50070, Morocco
- Team of Microbiology and Health, Laboratory of Chemistry-Biology Applied to the Environment, Faculty of Sciences, Moulay Ismail University, Meknes 50070, Morocco
| | - Fouzia Rhazi Filali
- Team of Microbiology and Health, Laboratory of Chemistry-Biology Applied to the Environment, Faculty of Sciences, Moulay Ismail University, Meknes 50070, Morocco
| | - Soumia Moujane
- Biochemistry of Natural Substances, Faculty of Science and Techniques, Moulay Ismail University, Errachdia 50003, Morocco
| | - Yassine Oulad El Majdoub
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy
| | - Philipp Otzen
- Institute of Anorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Souhail Channaoui
- Oasis System Research Unit, Regional Center of Agricultural Research of Errachidia, National Institute of Agricultural Research, P.O. Box 415, Rabat 10090, Morocco
| | - Abdelaziz Ed-Dra
- Laboratory of Engineering and Applied Technologies, Higher School of Technology, M’ghila Campus, Sultan Moulay Slimane University, Beni Mellal 23000, Morocco
| | - Toufik Bouddine
- Bioactive Molecules, Health and Biotechnology, Centre of Technology and Transformation, Faculty of Sciences, Moulay Ismail University, Meknes 50070, Morocco
| | - Khalid Sellam
- Biology, Environment and Health Team, Faculty of Sciences and Technologies, Moulay Ismail University, Meknes 50070, Morocco
| | - Ali Ait Boughrous
- Biology, Environment and Health Team, Faculty of Sciences and Technologies, Moulay Ismail University, Meknes 50070, Morocco
| | - Natalizia Miceli
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy
| | - Ammar B. Altemimi
- Food Science Department, College of Agriculture, University of Basrah, Basrah 61004, Iraq
| | - Francesco Cacciola
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98125 Messina, Italy
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13
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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14
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Albayrak E, Koçer S, Mutlu O. Identification of novel compounds against Acinetobacter baumannii 3-oxoacyl-[acyl-carrier-protein] synthase I (FabB) via comprehensive structure-based computational approaches. J Mol Graph Model 2023; 124:108565. [PMID: 37454410 DOI: 10.1016/j.jmgm.2023.108565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/18/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Acinetobacter baumannii is one of the most serious opportunistic pathogens according to WHO. The difference between bacterial and mammalian fatty acid biosynthesis pathways makes FASII enzymes attractive targets in drug discovery. 3-oxoacyl-[acyl-carrier-protein] synthase I (FabB) from the FAS II pathway catalyze the condensation of malonyl ACP with acyl-ACP, and elongates the fatty acid chain by two carbons. To investigate potential inhibitors of the A. baumannii FabB, we used computational approaches including homology modeling, high-throughput virtual screening, molecular docking, molecular dynamics simulations, and MM-GBSA free energy calculations. After the high-throughput virtual screening, the resulting ligands were further screened using the QM-polarized ligand docking (QPLD) and induced fit docking (IFD) approaches. Molecular dynamics simulations were performed for 100 ns. And according to binding free energy calculations, we have identified nine compounds with the best binding affinities. Three of these compounds were selected for an additional 1 μs MD simulation to assess ligand stability. Two of them named L6 and L7 showed promised stability and affinity to the target. Here, we present novel compounds against A. baumannii FabB via structure-based computational approaches. These compounds might pave the way for the design of new lead structures and inhibitors for multidrug-resistant A. baumannii.
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Affiliation(s)
- Esra Albayrak
- Marmara University, Faculty of Science, Department of Biology, Goztepe Campus, 34722, Kadikoy, Istanbul, Turkey
| | - Sinem Koçer
- Istanbul Yeni Yuzyil University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, 34010, Cevizlibag, Istanbul, Turkey
| | - Ozal Mutlu
- Marmara University, Faculty of Science, Department of Biology, Goztepe Campus, 34722, Kadikoy, Istanbul, Turkey.
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15
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Jiang Z, Chen A, Chen J, Sekhon A, Louie GV, Noel JP, La Clair JJ, Burkart MD. Masked cerulenin enables a dual-site selective protein crosslink. Chem Sci 2023; 14:10925-10933. [PMID: 37829009 PMCID: PMC10566503 DOI: 10.1039/d3sc02864j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023] Open
Abstract
Protein-reactive natural products such as the fungal metabolite cerulenin are recognized for their value as therapeutic candidates, due to their ability to selectively react with catalytic residues within a protein active site or a complex of protein domains. Here, we explore the development of fatty-acid and polyketide-synthase probes by synthetically modulating cerulenin's functional moieties. Using a mechanism-based approach, we reveal unique reactivity within cerulenin and adapt it for fluorescent labeling and crosslinking of fatty-acid and iterative type-I polyketide synthases. We also describe two new classes of silylcyanohydrin and silylhemiaminal masked crosslinking probes that serve as new tools for activity and structure studies of these biosynthetic pathways.
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Affiliation(s)
- Ziran Jiang
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Jeffrey Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Arman Sekhon
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Gordon V Louie
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - Joseph P Noel
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
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16
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Kasmawati H, Ruslin R, Arfan A, Sida NA, Saputra DI, Halimah E, Mustarichie R. Antibacterial Potency of an Active Compound from Sansevieria trifasciata Prain: An Integrated In Vitro and In Silico Study. Molecules 2023; 28:6096. [PMID: 37630348 PMCID: PMC10457997 DOI: 10.3390/molecules28166096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Sansevieria trifasciata Prain holds great potential as a valuable asset in pharmaceutical development. In this study, our focus is to explore and assess the antibacterial activity of various components derived from this plant, including extracts, fractions, subfractions, and isolates, explicitly targeting two common bacteria: Escherichia coli and Streptococcus aureus. The isolated compound, identified as a derivative pyridone alkaloid (5-methyl-11-(2-oxopyridin-1(2H)-yl)undecaneperoxoicacid), demonstrates notable antibacterial effects. The extracts, fractions, subfractions, and isolates reveal significant bacterial growth reductions (p < 0.05). The minimum inhibitory concentration (MIC) values for Escherichia coli were 1.95 ppm, 3.9 ppm, 15.62 ppm, and 7.81 ppm, respectively, while the MIC values for Streptococcus aureus were 1.95 ppm, 1.95 ppm, 15.62 ppm, and 7.81 ppm, respectively. Computational analysis showed the isolates' interaction with key residues on the active site of β-ketoacyl-ACP synthase from Escherichia coli and TyrRS from Streptococcus aureus. The findings indicate that the isolates exhibit a strong affinity for specific residues, including His333, Cys163, and Phe392 in β-ketoacyl-ACP synthase, as well as Arg88, His117, Glu160, and Gln213 in TyrRS. Comparative energy calculations using MMPBSA demonstrate the isolates' favorable binding energy (-104,101 kJ/mol for β-ketoacyl-ACP synthase and -81,060 kJ/mol for TyrRS) compared to ciprofloxacin. The elucidated antibacterial activity and molecular interactions of the isolates present valuable knowledge for future in vitro studies, facilitating the development of novel antibacterial agents targeting diverse bacterial strains.
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Affiliation(s)
- Henny Kasmawati
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Ruslin Ruslin
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Arfan Arfan
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Nurramadhani A. Sida
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Dimas Isnu Saputra
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Eli Halimah
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia;
| | - Resmi Mustarichie
- Department of Analytical Pharmacy and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
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17
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Ejaz SA, Aziz M, Wani TA, Al-Kahtani HM. Evaluation of mechanical features and antibacterial potential of fluoroquinolone against β-ketoacyl-ACP synthases (FabB, FabF & FabH) via computational approaches. Arch Biochem Biophys 2023:109674. [PMID: 37419193 DOI: 10.1016/j.abb.2023.109674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The synthesis of fatty acids, which are essential for the growth and survival of bacterial cells, is catalyzed by beta-keto acyl-ACP synthase I-III. Due to the significant differences between the bacterial ACP synthase enzyme and the mammalian enzyme, it may serve as a viable target for the development of potent anti-bacterial medications. In this study, a sophisticated molecular docking strategy was employed to target all three KAS enzymes. Initially, 1000 fluoroquinolone derivatives were obtained from PubChem database, along with the commonly used ciprofloxacin, and subjected to virtual screening against FabH, FabB, and FabF, respectively. Subsequently, molecular dynamics (MD) simulations were conducted to confirm the stability and reliability of the generated conformations. The compounds 155813629, 142486676, and 155567217 were found to exhibit potential molecular interactions against FabH, FabB, and FabF, respectively, with docking scores of -9.9, -8.9, and -9.9 kcal/mol. These scores outperformed the docking score of standard ciprofloxacin. Furthermore, MD simulations were used to assess the dynamic nature of molecular interactions in both physiological and dynamic settings. Throughout the simulated trajectory, all three complexes displayed favorable stability patterns. The findings of this investigation suggest that fluoroquinolone derivatives may serve as highly effective and selective inhibitors of the KAS enzyme.
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Affiliation(s)
- Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, the Islamia University of Bahawalpur, Saudi Arabia.
| | - Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, the Islamia University of Bahawalpur, Saudi Arabia
| | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Hammad M Al-Kahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
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18
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Sánchez-Lozano I, Muñoz-Cruz LC, Hellio C, Band-Schmidt CJ, Cruz-Narváez Y, Becerra-Martínez E, Hernández-Guerrero CJ. Metabolomic Insights of Biosurfactant Activity from Bacillus niabensis against Planktonic Cells and Biofilm of Pseudomonas stutzeri Involved in Marine Biofouling. Int J Mol Sci 2023; 24:ijms24044249. [PMID: 36835662 PMCID: PMC9965525 DOI: 10.3390/ijms24044249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
In marine environments, biofilm can cause negative impacts, including the biofouling process. In the search for new non-toxic formulations that inhibit biofilm, biosurfactants (BS) produced by the genus Bacillus have demonstrated considerable potential. To elucidate the changes that BS from B. niabensis promote in growth inhibition and biofilm formation, this research performed a nuclear magnetic resonance (NMR) metabolomic profile analysis to compare the metabolic differences between planktonic cells and biofilms of Pseudomonas stutzeri, a pioneer fouling bacteria. The multivariate analysis showed a clear separation between groups with a higher concentration of metabolites in the biofilm than in planktonic cells of P. stutzeri. When planktonic and biofilm stages were treated with BS, some differences were found among them. In planktonic cells, the addition of BS had a minor effect on growth inhibition, but at a metabolic level, NADP+, trehalose, acetone, glucose, and betaine were up-regulated in response to osmotic stress. When the biofilm was treated with the BS, a clear inhibition was observed and metabolites such as glucose, acetic acid, histidine, lactic acid, phenylalanine, uracil, and NADP+ were also up-regulated, while trehalose and histamine were down-regulated in response to the antibacterial effect of the BS.
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Affiliation(s)
- Ilse Sánchez-Lozano
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Luz Clarita Muñoz-Cruz
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Claire Hellio
- CNRS, IRD, Ifremer, LEMAR, Univ. Brest, Institut Universitaire Européen de la Mer, F-29280 Plouzané, France
| | - Christine J. Band-Schmidt
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
| | - Yair Cruz-Narváez
- Laboratorio de Posgrado de Operaciones Unitarias, Instituto Politécnico Nacional-ESIQIE-UPALM, Unidad Profesional Adolfo López Mateos, Edificio 7, 1.er Piso, Sección A, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
| | - Elvia Becerra-Martínez
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Av. Luis Enrique Erro S/N, Zacatenco, Delegación Gustavo A. Madero, Mexico City 07738, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
| | - Claudia J. Hernández-Guerrero
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. Instituto Politécnico Nacional S/N, Col. Playa Palo de Santa Rita, La Paz 23096, Mexico
- Correspondence: (E.B.-M.); (C.J.H.-G.)
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19
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Boram TJ, Benjamin AB, de Sousa AS, Stunkard LM, Stewart TA, Adams TJ, Craft NA, Velázquez-Marrero KG, Ling J, Nice JN, Lohman JR. Activity of Fatty Acid Biosynthesis Initiating Ketosynthase FabH with Acetyl/Malonyl-oxa/aza(dethia)CoAs. ACS Chem Biol 2023; 18:49-58. [PMID: 36626717 PMCID: PMC10311946 DOI: 10.1021/acschembio.2c00667] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fatty acid and polyketide biosynthetic enzymes exploit the reactivity of acyl- and malonyl-thioesters for catalysis. A prime example is FabH, which initiates fatty acid biosynthesis in many bacteria and plants. FabH performs an acyltransferase reaction with acetyl-CoA to generate an acetyl-S-FabH acyl-enzyme intermediate and subsequent decarboxylative Claisen-condensation with a malonyl-thioester carried by an acyl carrier protein (ACP). We envision that crystal structures of FabH with substrate analogues can provide insight into the conformational changes and enzyme/substrate interactions underpinning the distinct reactions. Here, we synthesize acetyl/malonyl-CoA analogues with esters or amides in place of the thioester and characterize their stability and behavior as Escherichia coli FabH substrates or inhibitors to inform structural studies. We also characterize the analogues with mutant FabH C112Q that mimics the acyl-enzyme intermediate allowing dissection of the decarboxylation reaction. The acetyl- and malonyl-oxa(dethia)CoA analogues undergo extremely slow hydrolysis in the presence of FabH or the C112Q mutant. Decarboxylation of malonyl-oxa(dethia)CoA by FabH or C112Q mutant was not detected. The amide analogues were completely stable to enzyme activity. In enzyme assays with acetyl-CoA and malonyl-CoA (rather than malonyl-ACP) as substrates, acetyl-oxa(dethia)CoA is surprisingly slightly activating, while acetyl-aza(dethia)CoA is a moderate inhibitor. The malonyl-oxa/aza(dethia)CoAs are inhibitors with Ki's near the Km of malonyl-CoA. For comparison, we determine the FabH catalyzed decomposition rates for acetyl/malonyl-CoA, revealing some fundamental catalytic traits of FabH, including hysteresis for malonyl-CoA decarboxylation. The stability and inhibitory properties of the substrate analogues make them promising for structure-function studies to reveal fatty acid and polyketide enzyme/substrate interactions.
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Affiliation(s)
- Trevor J. Boram
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Aaron B. Benjamin
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Amanda Silva de Sousa
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Lee M. Stunkard
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Taylor A. Stewart
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Timothy J. Adams
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Nicholas A. Craft
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Kevin G. Velázquez-Marrero
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Jianheng Ling
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Jaelen N. Nice
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Jeremy R. Lohman
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
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Implications of Fragment-Based Drug Discovery in Tuberculosis and HIV. Pharmaceuticals (Basel) 2022; 15:ph15111415. [PMID: 36422545 PMCID: PMC9692459 DOI: 10.3390/ph15111415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis (TB) remains a global health problem and the emergence of HIV has further worsened it. Long chemotherapy and the emergence of drug-resistance strains of Mycobacterium tuberculosis as well as HIV has aggravated the problem. This demands urgent the need to develop new anti-tuberculosis and antiretrovirals to treat TB and HIV. The lack of diversity in drugs designed using traditional approaches is a major disadvantage and limits the treatment options. Therefore, new technologies and approaches are required to solve the current issues and enhance the production of drugs. Interestingly, fragment-based drug discovery (FBDD) has gained an advantage over high-throughput screenings as FBDD has enabled rapid and efficient progress to develop potent small molecule compounds that specifically bind to the target. Several potent inhibitor compounds of various targets have been developed using FBDD approach and some of them are under progression to clinical trials. In this review, we emphasize some of the important targets of mycobacteria and HIV. We also discussed about the target-based druggable molecules that are identified using the FBDD approach, use of these druggable molecules to identify novel binding sites on the target and assays used to evaluate inhibitory activities of these identified druggable molecules on the biological activity of the targets.
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21
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Nickels JD, Bonifer KS, Tindall RR, Yahya A, Tan L, Do C, Davison BH, Elkins JG. Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF). Front Mol Biosci 2022; 9:1011981. [DOI: 10.3389/fmolb.2022.1011981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure—and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis, using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (ΔfadN) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA-fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n16:0 to a15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.
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22
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Ahmad W, Ansari MA, Yusuf M, Amir M, Wahab S, Alam P, Alomary MN, Alhuwayri AA, Khan M, Ali A, Warsi MH, Ashraf K, Ali M. Antibacterial, Anticandidal, and Antibiofilm Potential of Fenchone: In Vitro, Molecular Docking and In Silico/ADMET Study. PLANTS (BASEL, SWITZERLAND) 2022; 11:2395. [PMID: 36145798 PMCID: PMC9505686 DOI: 10.3390/plants11182395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
The aim of the present study is to investigate the effective antimicrobial and antibiofilm properties of fenchone, a biologically active bicyclic monoterpene, against infections caused by bacteria and Candida spp. The interactions between fenchone and three distinct proteins from Escherichia coli (β-ketoacyl acyl carrier protein synthase), Candida albicans (1, 3-β−D-glucan synthase), and Pseudomonas aeruginosa (Anthranilate-CoA ligase) were predicted using molecular docking and in silico/ADMET methods. Further, to validate the in-silico prediction, the antibacterial and antifungal potential of fenchone was evaluated against E. coli, P. aeruginosa, and C. albicans by determining minimum inhibitory concentration (MIC), minimum bacterial concentration (MBC), and minimum fungicidal concentration (MFC). The lowest MIC/MBC values of fenchone against E. coli and P. aeruginosa obtained was 8.3 ± 3.6/25 ± 0.0 and 266.6 ± 115.4/533.3 ± 230.9 mg/mL, respectively, whereas the MIC/MFC value for C. albicans was found to be 41.6 ± 14.4/83.3 ± 28.8 mg/mL. It was observed that fenchone has a significant effect on antimicrobial activity (p < 0.05). Our findings demonstrated that fenchone at 1 mg/mL significantly reduced the production of biofilm (p < 0.001) in E. coli, P. aeruginosa, and C. albicans by 70.03, 64.72, and 61.71%, respectively, in a dose-dependent manner when compared to control. Based on these results, it has been suggested that the essential oil from plants can be a great source of pharmaceutical ingredients for developing new antimicrobial drugs.
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Affiliation(s)
- Wasim Ahmad
- Department of Pharmacy, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Mohammad Yusuf
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Taif 21944, Saudi Arabia
| | - Mohd Amir
- Department of Natural Products and Alternative Medicine, College of Clinical Pharmacy, Imam Abdul Rahman bin Faisal University, Dammam 31441, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - Prawez Alam
- Department of Pharmacognosy, College of Pharmacy, Prince-Sattam Bin-Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mohammad N. Alomary
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | | | - Maria Khan
- Department of Pharmacognosy, R.V. Northland Institute, Dadri 203207, India
| | - Abuzer Ali
- Department of Pharmacognosy, College of Pharmacy, Taif University, Taif 21944, Saudi Arabia
| | - Musarrat Husain Warsi
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif 21944, Saudi Arabia
| | - Kamran Ashraf
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Cawangan Selangor, Kampus Puncak Alam, Bandar Puncak Alam 42300, Selangor Darul Ehsan, Malaysia
| | - Maksood Ali
- Department of Pharmacognosy, Orlean College of Pharmacy 42, Knowledge Park—III, Greater Noida 201308, India
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Abstract
Antibiotic resistance is a serious public health concern, and new drugs are needed to ensure effective treatment of many bacterial infections. Bacterial type II fatty acid synthesis (FASII) is a vital aspect of bacterial physiology, not only for the formation of membranes but also to produce intermediates used in vitamin production. Nature has evolved a repertoire of antibiotics inhibiting different aspects of FASII, validating these enzymes as potential targets for new antibiotic discovery and development. However, significant obstacles have been encountered in the development of FASII antibiotics, and few FASII drugs have advanced beyond the discovery stage. Most bacteria are capable of assimilating exogenous fatty acids. In some cases they can dispense with FASII if fatty acids are present in the environment, making the prospects for identifying broad-spectrum drugs against FASII targets unlikely. Single-target, pathogen-specific FASII drugs appear the best option, but a major drawback to this approach is the rapid acquisition of resistance via target missense mutations. This complication can be mitigated during drug development by optimizing the compound design to reduce the potential impact of on-target missense mutations at an early stage in antibiotic discovery. The lessons learned from the difficulties in FASII drug discovery that have come to light over the last decade suggest that a refocused approach to designing FASII inhibitors has the potential to add to our arsenal of weapons to combat resistance to existing antibiotics.
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Affiliation(s)
- Christopher D Radka
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; ,
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24
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Z. Officinale-Doped Silver/Calcium Oxide Nanocomposites: Catalytic Activity and Antimicrobial Potential with Molecular Docking Analysis. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.07.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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25
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Fucoxanthin’s Optimization from Undaria pinnatifida Using Conventional Heat Extraction, Bioactivity Assays and In Silico Studies. Antioxidants (Basel) 2022; 11:antiox11071296. [PMID: 35883788 PMCID: PMC9311727 DOI: 10.3390/antiox11071296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Brown macroalgae are a potential source of natural pigments. Among them, Undaria pinnatifida is recognized for its high concentration of fucoxanthin (Fx), which is a pigment with a wide range of bioactivities. In this study, three independent parameters were optimized for conventional heat extraction (CHE) to maximize the recovery of Fx from Undaria pinnatifida. Optimal conditions (temperature = 45 °C, solvent = 70%, and time = 61 min) extracted 5.1 mg Fx/g dw. Later, the bioactivities of the Fx-rich extracts (antioxidant, antimicrobial, and neuroprotective) were assessed using in vitro and in silico approaches. In vitro assays indicated that Fx has a strong antioxidant capacity and even stronger antimicrobial activity against gram-positive bacteria. This data was supported in silico where Fx established a high binding affinity to DR, a Staphylococcus aureus protein, through aa ALA-8, LEU-21, and other alkane interactions. Finally, the in vitro enzymatic inhibition of AChE using Fx, was further supported using docking models that displayed Fx as having a high affinity for aa TYR72 and THR 75; therefore, the Fx extraction behavior explored in this work may reduce the costs associated with energy and solvent consumption. Moreover, this paper demonstrates the efficiency of CHE when recovering high amounts of Fx from Undaria pinnatifida. Furthermore, these findings can be applied in different industries.
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El-Lateef HMA, Khalaf MM, Shehata MR, Abu-Dief AM. Fabrication, DFT Calculation, and Molecular Docking of Two Fe(III) Imine Chelates as Anti-COVID-19 and Pharmaceutical Drug Candidate. Int J Mol Sci 2022; 23:ijms23073994. [PMID: 35409353 PMCID: PMC8999679 DOI: 10.3390/ijms23073994] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/01/2023] Open
Abstract
Two tetradentate dibasic chelating Schiff base iron (III) chelates were prepared from the reaction of 2,2′-((1E,1′E)-(1,2-phenylenebis(azanylylidene))bis(methanylylidene))bis(4-bromophenol) (PDBS) and 2,2′-((1E,1′E)-((4-chloro-1,2-phenylene)bis(azanylylidene))-bis(methanylylidene))bis(4-bromophenol) (CPBS) with Fe3+ ions. The prepared complexes were fully characterized with spectral and physicochemical tools such as IR, NMR, CHN analysis, TGA, UV-visible spectra, and magnetic moment measurements. Moreover, geometry optimizations for the synthesized ligands and complexes were conducted using the Gaussian09 program through the DFT approach, to find the best structures and key parameters. The prepared compounds were tested as antimicrobial agents against selected strains of bacteria and fungi. The results suggests that the CPBSFe complex has the highest activity, which is close to the reference. An MTT assay was used to screen the newly synthesized compounds against a variety of cell lines, including colon cancer cells, hepatic cellular carcinoma cells, and breast carcinoma cells. The results are expressed by IC50 value, in which the 48 µg/mL value of the CPBSFe complex indicates its success as a potential anticancer agent. The antioxidant behavior of the two imine chelates was studied by DPPH assay. All the tested imine complexes show potent antioxidant activity compared to the standard Vitamin C. Furthermore, the in vitro assay and the mechanism of binding and interaction efficiency of the tested samples with the receptor of COVID-19 core protease viral protein (PDB ID: 6lu7) and the receptor of Gram-negative bacteria (Escherichia coli, PDB ID: 1fj4) were investigated using molecular docking experiments.
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Affiliation(s)
- Hany M. Abd El-Lateef
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia;
- Chemistry Department, Faculty of Science, Sohag University, Sohag 82534, Egypt
- Correspondence: (H.M.A.E.-L.); (A.M.A.-D.)
| | - Mai M. Khalaf
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia;
- Chemistry Department, Faculty of Science, Sohag University, Sohag 82534, Egypt
| | - Mohamed R. Shehata
- Chemistry Department, Faculty of Science, Cairo University, Giza P.O. Box 12613, Egypt;
| | - Ahmed M. Abu-Dief
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 400, Al-Ahsa 31982, Saudi Arabia;
- Chemistry Department, College of Science, Taibah University, Madinah P.O. Box 344, Saudi Arabia
- Correspondence: (H.M.A.E.-L.); (A.M.A.-D.)
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Li S, Rong L, Wang S, Liu S, Lu Z, Miao L, Zhao B, Zhang C, Xiao D, Pushpanathan K, Wong A, Yu A. Enhanced limonene production by metabolically engineered Yarrowia lipolytica from cheap carbon sources. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.117342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Abdou A, Idouaarame S, Salah M, Nor N, Zahm, S, Maksoudi AE, Mazoir N, benharref A, Dari A, Eddine JJ, Blaghen M, Dakir M. Phytochemical study: molecular docking of eugenol derivatives as antioxidant and antimicrobial agents. LETT ORG CHEM 2022. [DOI: 10.2174/1570178619666220111112125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
Eugenol (4-allyl-2-methoxyphenol) is a natural phenolic compound present in certain aromatic plants; however, it is generally extracted from essential oil of Eugenia caryophyllata (Syzygiumaromaticum) (L.) Merr. and L.M. Perry. This bioactive natural compound has generated considerable biological interest with well-known antimicrobial and antioxidant actions. The authors have aimed to the evaluations of eugenol derivatives and their as antimicrobial and antioxidant agent with the aid of molecular dynamic simulation. The starting material was extracted from cloves using hydrodistillation. Two eugenol derivatives, acetyleugenol (4-allyl-2-methoxyphenylacetate) and epoxyeugenol (4-allyl-2-methoxyphenol) were prepared and tested against two strains Escherichia coli (E. Coli) and Staphylococcus aureus (S. Aureus). The results have revealed that the three compounds (Eugenol, acetyleugenol and epoxyeugenol) possess important potentials of inhibition against E. coli and S. Aureus. The antioxidant activity of eugenol derivatives was evaluated by the reaction with DPPH (1,1-diphenyl-2-picrylhydrazyl), showed that the epoxyeugenol was the most active compound. The molecular docking scores of three compounds and the amino acids in the active site pockets of the selected proteins of the two bacteria have approved and explain the biological experimental outcomes.
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Affiliation(s)
- Achraf Abdou
- Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
| | - Sabrine Idouaarame
- Laboratory of pharmacology, microbiology, Biotechnology and environment, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
| | - Mohammed Salah
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, P.O. Box 20, 24000 El Jadida, Morocco
| | - Nabil Nor
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, P.O. Box 20, 24000 El Jadida, Morocco
| | - Soukaina Zahm,
- Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
| | - Abdelhakim El Maksoudi
- Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
| | - Noureddine Mazoir
- Laboratory of Plant Biotechnology and Ecosystem Valorization, Faculty of Sciences Chouaib Doukkali University, Research Unit: Natural Resource Valorizations P.O. Box 20, 24000 El Jadida, Morocco
| | - Ahmed benharref
- Laboratory of Biomolecular Chemistry, Natural Substances and Reactivity, URAC 16, Faculty of Sciences Semlalia, Cadi Ayyad University, P.O. Box 2390, 40000 Marrakech, Morocco
| | - Abdelmjid Dari
- Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
| | - Jamal Jamal Eddine
- Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
| | - Mohamed Blaghen
- Laboratory of pharmacology, microbiology, Biotechnology and environment, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
| | - Mohamed Dakir
- Laboratory of Organic Synthesis, Extraction and Valorization, Faculty of Sciences Ain Chock, Hassan II University, P.O. Box 20, 20000, Casablanca, Morocco
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29
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Maitra N, Hammer S, Kjerfve C, Bankaitis VA, Polymenis M. Translational control of lipogenesis links protein synthesis and phosphoinositide signaling with nuclear division in Saccharomyces cerevisiae. Genetics 2022; 220:iyab171. [PMID: 34849864 PMCID: PMC8733439 DOI: 10.1093/genetics/iyab171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Continuously dividing cells coordinate their growth and division. How fast cells grow in mass determines how fast they will multiply. Yet, there are few, if any, examples of a metabolic pathway that actively drives a cell cycle event instead of just being required for it. Here, we show that translational upregulation of lipogenic enzymes in Saccharomyces cerevisiae increased the abundance of lipids and promoted nuclear elongation and division. Derepressing translation of acetyl-CoA carboxylase and fatty acid synthase also suppressed cell cycle-related phenotypes, including delayed nuclear division, associated with Sec14p phosphatidylinositol transfer protein deficiencies, and the irregular nuclear morphologies of mutants defective in phosphatidylinositol 4-OH kinase activities. Our results show that increased lipogenesis drives a critical cell cycle landmark and report a phosphoinositide signaling axis in control of nuclear division. The broad conservation of these lipid metabolic and signaling pathways raises the possibility these activities similarly govern nuclear division in other eukaryotes.
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Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Staci Hammer
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Clara Kjerfve
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vytas A Bankaitis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular & Cellular Medicine, Texas A&M Health Sciences Center, College Station, TX 77843, USA
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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Shinde R, Suvarna V. Fatty Acid Biosynthesis: An Updated Review on KAS Inhibitors. Curr Drug Discov Technol 2022; 19:e110122200137. [PMID: 35021976 DOI: 10.2174/1570163819666220111113032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
Since the early twentieth century, with the isolation of penicillin and streptomycin in the 1940s, the modern era of anti-infective drug development has gained momentum. Due to the enormous success of early drug discovery, many infectious diseases were successfully prevented and eradicated. However, this initial hope was wrongheaded, and pathogens evolved as a significant threat to human health. Drug resistance develops as a result of natural selection's relentless pressure, necessitating the identification of new drug targets and the creation of chemotherapeutics that bypass existing drug resistance mechanisms. Fatty acid biosynthesis (FAS) is a crucial metabolic mechanism for bacteria during their growth and development. Several crucial enzymes involved in this biosynthetic pathway have been identified as potential targets for new antibacterial agents. In Escherichia coli (E. coli), this pathway has been extensively investigated. The present review focuses on progress in the development of Kas A, Kas B, and Fab H inhibitors as mono-therapeutic antibiotics.
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Affiliation(s)
- Rani Shinde
- Department of Quality Assurance, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai University, Mumbai, India
| | - Vasanti Suvarna
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai University, Mumbai, India
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31
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Abdel-Rahman LH, Basha MT, Al-Farhan BS, Shehata MR, Mohamed SK, Ramli Y. [Cu(dipicolinoylamide)(NO3)(H2O)] as anti-COVID-19 and antibacterial drug candidate: Design, synthesis, crystal structure, DFT and molecular docking. J Mol Struct 2022; 1247:131348. [PMID: 36406284 PMCID: PMC9640988 DOI: 10.1016/j.molstruc.2021.131348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
For first time the new N-picolinoypicolinlamide was obtained as in situ ligand during the reaction of 2,4,6-ris(2-pyridyl)-,3,5-triazine with aqueous solution of CuNO3·3H2O and formed the corresponding complex [Cu(dipicolinoylamide)(NO3)(H2O)]. The crystal structure of the obtained complex was determined by x-ray structure. The complex crystallizes in space group P21/n, a = 10.2782(9) Å, b = 7.5173(6) Å, c = 17.738(2) Å, α = 90.00°, β = 91.368(1)°, γ = 90.00°, V = 1370.1(2) Å3, Z = 4. The copper center has a distorted octahedral geometry. DFT calculations show good agreement between theoretical and X-ray data. The Molecular docking studies were executed to consider the nature of binding and binding affinity of the synthesized compounds with the receptor of COVID-19 main protease viral protein (PDB ID: 6lu7), the receptor of gram –ve bacteria (Escherichia coli, PDB ID: 1fj4) and the receptor of gram +ve bacteria (Staphylococcus aureus, PDB ID: 3q8u and Proteus PDB ID: 5i39) and with human DNA. Finally, in silico ADMET predictions was also examined.
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Affiliation(s)
| | - Maram T Basha
- University of Jeddah, College of Science, Department of Chemistry, Jeddah, Saudi Arabia
| | - Badriah Saad Al-Farhan
- Chemistry Department, Faculty of Girls for Science, King Khalid University, Abha, Saudi Arabia
| | - Mohamed R Shehata
- Chemistry Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 6GD, England
- Chemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt
| | - Youssef Ramli
- Laboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
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32
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Hemamalini M, Kestek İ, Çınar EB, Agar AA, Dege N, Josekavitha S, Rajakannan V. Chemical Synthesis, X-ray Crystallography, Hirshfeld Surface Analysis, and Molecular Docking Studies of (E)-2-(((3-Bromophenyl)imino)methyl)-5-(diethylamino)phenol Schiff Base. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521060158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Shoukry MM, Shehata MR, Abdel Wahab AM. Synthesis, characterization, thermal degradation, docking,
DFT
calculation, and biological activity of dimethyltin(
IV
) complex with homopiperazine. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mohamed M. Shoukry
- Department of Chemistry, Faculty of Science University of Cairo Giza Egypt
| | - Mohamed R. Shehata
- Department of Chemistry, Faculty of Science University of Cairo Giza Egypt
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Espeland LO, Georgiou C, Klein R, Bhukya H, Haug BE, Underhaug J, Mainkar PS, Brenk R. An Experimental Toolbox for Structure-Based Hit Discovery for P. aeruginosa FabF, a Promising Target for Antibiotics. ChemMedChem 2021; 16:2715-2726. [PMID: 34189850 PMCID: PMC8518799 DOI: 10.1002/cmdc.202100302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/22/2021] [Indexed: 12/12/2022]
Abstract
FabF (3-oxoacyl-[acyl-carrier-protein] synthase 2), which catalyses the rate limiting condensation reaction in the fatty acid synthesis II pathway, is an attractive target for new antibiotics. Here, we focus on FabF from P. aeruginosa (PaFabF) as antibiotics against this pathogen are urgently needed. To facilitate exploration of this target we have set up an experimental toolbox consisting of binding assays using bio-layer interferometry (BLI) as well as saturation transfer difference (STD) and WaterLOGSY NMR in addition to robust conditions for structure determination. The suitability of the toolbox to support structure-based design of FabF inhibitors was demonstrated through the validation of hits obtained from virtual screening. Screening a library of almost 5 million compounds resulted in 6 compounds for which binding into the malonyl-binding site of FabF was shown. For one of the hits, the crystal structure in complex with PaFabF was determined. Based on the obtained binding mode, analogues were designed and synthesised, but affinity could not be improved. This work has laid the foundation for structure-based exploration of PaFabF.
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Affiliation(s)
- Ludvik Olai Espeland
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
- Department of ChemistryUniversity of BergenAllégaten 415007BergenNorway
| | - Charis Georgiou
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
| | - Raphael Klein
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
- Institute of Pharmacy and BiochemistryJohannes Gutenberg UniversityStaudingerweg 555128MainzGermany
| | - Hemalatha Bhukya
- Department of Organic Synthesis & Process ChemistryCSIR-Indian Institute of Chemical TechnologyTarnakaHyderabad500007India
| | - Bengt Erik Haug
- Department of ChemistryUniversity of BergenAllégaten 415007BergenNorway
| | - Jarl Underhaug
- Department of ChemistryUniversity of BergenAllégaten 415007BergenNorway
| | - Prathama S. Mainkar
- Department of Organic Synthesis & Process ChemistryCSIR-Indian Institute of Chemical TechnologyTarnakaHyderabad500007India
| | - Ruth Brenk
- Department of BiomedicineUniversity of BergenJonas Lies Vei 915020BergenNorway
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35
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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36
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Han J, Liu X, Zhang L, Quinn RJ, Feng Y. Anti-mycobacterial natural products and mechanisms of action. Nat Prod Rep 2021; 39:77-89. [PMID: 34226909 DOI: 10.1039/d1np00011j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to June, 2020Tuberculosis (TB) continues to be a major disease with high mortality and morbidity globally. Drug resistance and long duration of treatment make antituberculosis drug discovery more challenging. In this review, we summarize recent advances on anti-TB natural products (NPs) and their potential molecular targets in cell wall synthesis, protein production, energy generation, nucleic acid synthesis and other emerging areas. We highlight compounds with activity against drug-resistant TB, and reveal several novel targets including Mtb biotin synthase, ATP synthase, 1,4-dihydroxy-2-naphthoate prenyltransferase and biofilms. These anti-TB NPs and their targets could facilitate target-based screening and accelerate TB drug discovery.
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Affiliation(s)
- Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
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37
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Paiva P, Medina FE, Viegas M, Ferreira P, Neves RPP, Sousa JPM, Ramos MJ, Fernandes PA. Animal Fatty Acid Synthase: A Chemical Nanofactory. Chem Rev 2021; 121:9502-9553. [PMID: 34156235 DOI: 10.1021/acs.chemrev.1c00147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.
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Affiliation(s)
- Pedro Paiva
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Fabiola E Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
| | - Matilde Viegas
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro Ferreira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Rui P P Neves
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - João P M Sousa
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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38
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Mindrebo JT, Chen A, Kim WE, Re RN, Davis TD, Noel JP, Burkart MD. Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases. ACS Catal 2021; 11:6787-6799. [DOI: 10.1021/acscatal.1c00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Rebecca N. Re
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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39
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Troudi A, Pagès JM, Brunel JM. Chemical Highlights Supporting the Role of Lipid A in Efficient Biological Adaptation of Gram-Negative Bacteria to External Stresses. J Med Chem 2021; 64:1816-1834. [PMID: 33538159 DOI: 10.1021/acs.jmedchem.0c02185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria provides an efficient barrier against external noxious compounds such as antimicrobial agents. Associated with drug target modification, it contributes to the overall failure of chemotherapy. In the complex OM architecture, Lipid A plays an essential role by anchoring the lipopolysaccharide in the membrane and ensuring the spatial organization between lipids, proteins, and sugars. Currently, the targets of almost all antibiotics are intracellularly located and require translocation across membranes. We report herein an integrated view of Lipid A synthesis, membrane assembly, a structure comparison at the molecular structure level of numerous Gram-negative bacterial species, as well as its recent use as a target for original antibacterial molecules. This review paves the way for a new vision of a key membrane component that acts during bacterial adaptation to environmental stresses and for the development of new weapons against microbial resistance to usual antibiotics.
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Affiliation(s)
- Azza Troudi
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France.,Laboratory of Microorganisms and Active Biomolecules, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1008, Tunisia
| | - Jean Marie Pagès
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| | - Jean Michel Brunel
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
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40
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Cloning, characterization, and functional analysis of acetyl-CoA C-acetyltransferase and 3-hydroxy-3-methylglutaryl-CoA synthase genes in Santalum album. Sci Rep 2021; 11:1082. [PMID: 33441887 PMCID: PMC7807033 DOI: 10.1038/s41598-020-80268-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
Sandalwood (Santalum album L.) is famous for its unique fragrance derived from the essential oil of heartwood, whose major components are santalols. To understand the mechanism underlying the biosynthesis of santalols, in this study, we cloned two related genes involved in the mevalonate pathway in S. album coding for acetyl-CoA C-acetyl transferase (AACT) and 3-hydroxy-3-methyglutary-CoA synthase (HMGS). These genes were characterized and functionally analyzed, and their expression profiles were also assessed. An AACT gene designated as SaAACT (GenBank accession No. MH018694) and a HMGS gene designated as SaHMGS (GenBank accession No. MH018695) were successfully cloned from S. album. The deduced SaAACT and SaHMGS proteins contain 415 and 470 amino acids, and the corresponding size of their open-reading frames is 1538 bp and 1807 bp, respectively. Phylogenetic trees showed that the SaAACT protein had the closest relationship with AACT from Hevea brasiliensis and the SaHMGS proteins had the highest homology with HMGS from Siraitia grosvenorii. Functional complementation of SaAACT and SaHMGS in a mutant yeast strain deficient in these proteins confirmed that SaAACT and SaHMGS cDNA encodes functional SaAACT and SaHMGS that mediate mevalonate biosynthesis in yeast. Tissue-specific expression analysis revealed that both genes were constitutively expressed in all examined tissues (roots, sapwood, heartwood, young leaves, mature leaves and shoots) of S. album, both genes showing highest expression in roots. After S. album seedlings were treated with 100 μM methyl jasmonate, the expression levels of SaAACT and SaHMGS genes increased, suggesting that these genes were responsive to this elicitor. These studies provide insight that would allow further analysis of the role of genes related to the sandalwood mevalonate pathway in the regulation of biosynthesis of sandalwood terpenoids and a deeper understanding of the molecular mechanism of santalol biosynthesis.
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41
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Cogan DP, Ly J, Nair SK. Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation. ACS Chem Biol 2020; 15:2783-2791. [PMID: 33017142 DOI: 10.1021/acschembio.0c00579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While several bioactive natural products that contain tetramate or pyridone heterocycles have been described, information on the enzymology underpinning these functionalities has been limited. Here we biochemically characterize an off-loading Dieckmann cyclase, NcmC, that installs the tetramate headgroup in nocamycin, a hybrid polyketide/nonribosomal peptide natural product. Crystal structures of the enzyme (1.6 Å) and its covalent complex with the epoxide cerulenin (1.6 Å) guide additional structure-based mutagenesis and product-profile analyses. Our results offer mechanistic insights into how the conserved thioesterase-like scaffold has been adapted to perform a new chemical reaction, namely, heterocyclization. Additional bioinformatics combined with docking and modeling identifies likely candidates for heterocycle formation in underexplored gene clusters and uncovers a modular basis of substrate recognition by the two subdomains of these Dieckmann cyclases.
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42
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GUPTA S, UNDALE VR, LAKHADIVE K. Novel Targets for Antimicrobials. Turk J Pharm Sci 2020; 17:565-575. [PMID: 33177939 PMCID: PMC7650728 DOI: 10.4274/tjps.galenos.2020.90197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 04/21/2020] [Indexed: 12/01/2022]
Abstract
Antimicrobial resistance (AMR) is the phenomenon developed by microorganism on exposure to antimicrobial agents, making them unresponsive. Development of microbial confrontation is a severe rising risk to global community well-being as treatment in addition, management of such resistant microbial infections is difficult and challenging. The situation requires action across all government sectors and society. The change in the molecular target on which antimicrobial drugs act is one of the key mechanisms behind AMR. One of the approaches to battle with AMR can be exploring newer molecular targets in microbes and discovering new molecules accordingly. There are various examples of novel targets such as biomolecules involving in biosynthesis of cell wall, biosynthesis of aromatic amino acid, cell disunion, biosynthesis of fatty acid, and isoprenoid biosynthesis and tRNA synthetases. Fatty acid biosynthesis (FAB) and their enzymes among all the above is the more appealing target for the advancement of new antimicrobial agents. Number of promising inhibitors have been developed for bacterial fatty acid synthesis (FAS) and also few of them are clinically used. Some of these potential inhibitors are found to be used in development of new antibacterial as a lead compound and have been discovered from high throughput screening processes like Platencimycin and their analogue, Platencin. The review majorly encompasses bacterial FAB in type II FAS system and potential inhibitors with respective targets of novel antibacterial.
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Affiliation(s)
- Suchita GUPTA
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra
| | | | - Kedar LAKHADIVE
- Dr. D.Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, Maharashtra
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43
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A kinetic rationale for functional redundancy in fatty acid biosynthesis. Proc Natl Acad Sci U S A 2020; 117:23557-23564. [PMID: 32883882 DOI: 10.1073/pnas.2013924117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells build fatty acids with biocatalytic assembly lines in which a subset of enzymes often exhibit overlapping activities (e.g., two enzymes catalyze one or more identical reactions). Although the discrete enzymes that make up fatty acid pathways are well characterized, the importance of catalytic overlap between them is poorly understood. We developed a detailed kinetic model of the fatty acid synthase (FAS) of Escherichia coli and paired that model with a fully reconstituted in vitro system to examine the capabilities afforded by functional redundancy in fatty acid synthesis. The model captures-and helps explain-the effects of experimental perturbations to FAS systems and provides a powerful tool for guiding experimental investigations of fatty acid assembly. Compositional analyses carried out in silico and in vitro indicate that FASs with multiple partially redundant enzymes enable tighter (i.e., more independent and/or broader range) control of distinct biochemical objectives-the total production, unsaturated fraction, and average length of fatty acids-than FASs with only a single multifunctional version of each enzyme (i.e., one enzyme with the catalytic capabilities of two partially redundant enzymes). Maximal production of unsaturated fatty acids, for example, requires a second dehydratase that is not essential for their synthesis. This work provides a kinetic, control-theoretic rationale for the inclusion of partially redundant enzymes in fatty acid pathways and supplies a valuable framework for carrying out detailed studies of FAS kinetics.
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44
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Yan Y, Liu N, Tang Y. Recent developments in self-resistance gene directed natural product discovery. Nat Prod Rep 2020; 37:879-892. [PMID: 31912842 PMCID: PMC7340575 DOI: 10.1039/c9np00050j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2019Natural products (NPs) are important sources of human therapeutic agents and pesticides. To prevent self-harm from bioactive NPs, some microbial producers employ self-resistance genes to protect themselves. One effective strategy is to employ a self-resistance enzyme (SRE), which is a slightly mutated version of the original metabolic enzyme, and is resistant to the toxic NP but is still functional. The presence of a SRE in a gene cluster can serve as a predictive window to the biological activity of the NPs synthesized by the pathway. In this highlight, we summarize representative examples of NP biosynthetic pathways that utilize self-resistance genes for protection. Recent discoveries based on self-resistance gene identification have helped in bridging the gap between activity-guided and genome-driven approaches for NP discovery and functional assignment.
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Affiliation(s)
- Yan Yan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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45
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Nickels JD, Poudel S, Chatterjee S, Farmer A, Cordner D, Campagna SR, Giannone RJ, Hettich RL, Myles DAA, Standaert RF, Katsaras J, Elkins JG. Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome. Front Microbiol 2020; 11:914. [PMID: 32499768 PMCID: PMC7243436 DOI: 10.3389/fmicb.2020.00914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/17/2020] [Indexed: 12/22/2022] Open
Abstract
Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells – as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins.
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Affiliation(s)
- Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, United States
| | - Suresh Poudel
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sneha Chatterjee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Abigail Farmer
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Destini Cordner
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, United States
| | - Shawn R Campagna
- Department of Chemistry, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biological and Small Molecule Mass Spectrometry Core, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dean A A Myles
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert F Standaert
- Department of Chemistry, East Tennessee State University, Johnson City, TN, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Shull Wollan Center - a Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Physics and Astronomy, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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46
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Milke L, Marienhagen J. Engineering intracellular malonyl-CoA availability in microbial hosts and its impact on polyketide and fatty acid synthesis. Appl Microbiol Biotechnol 2020; 104:6057-6065. [PMID: 32385515 PMCID: PMC7316851 DOI: 10.1007/s00253-020-10643-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022]
Abstract
Malonyl-CoA is an important central metabolite serving as the basic building block for the microbial synthesis of many pharmaceutically interesting polyketides, but also fatty acid-derived compounds including biofuels. Especially Saccharomyces cerevisiae, Escherichia coli, and Corynebacterium glutamicum have been engineered towards microbial synthesis of such compounds in recent years. However, developed strains and processes often suffer from insufficient productivity. Usually, tightly regulated intracellular malonyl-CoA availability is regarded as the decisive bottleneck limiting overall product formation. Therefore, metabolic engineering towards improved malonyl-CoA availability is essential to design efficient microbial cell factories for the production of polyketides and fatty acid derivatives. This review article summarizes metabolic engineering strategies to improve intracellular malonyl-CoA formation in industrially relevant microorganisms and its impact on productivity and product range, with a focus on polyketides and other malonyl-CoA-dependent products.Key Points• Malonyl-CoA is the central building block of polyketide synthesis.• Increasing acetyl-CoA supply is pivotal to improve malonyl-CoA availability.• Improved acetyl-CoA carboxylase activity increases availability of malonyl-CoA.• Fatty acid synthesis as an ambivalent target to improve malonyl-CoA supply.
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Affiliation(s)
- Lars Milke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany. .,Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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47
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Charov K, Burkart MD. Quantifying protein-protein interactions of the acyl carrier protein with solvatochromic probes. Methods Enzymol 2020; 638:321-340. [PMID: 32416920 DOI: 10.1016/bs.mie.2020.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Protein-protein interactions (PPIs) are universal to life and their study and understanding is critical to drug discovery and bioengineering efforts. Historically, X-ray crystallography, isothermal titration calorimetry and other biophysical methods have been used to study PPIs, but can be costly and are low throughput, hindering progress towards rapid evaluation of these interactions. Recent interest in targeting PPIs and in engineering biosynthetic pathways in which PPIs play a critical role has driven innovation in their evaluation but a universal screen is still needed. One of the best characterized systems relying upon PPIs is Escherichia coli type II fatty acid biosynthesis in which the central acyl carrier protein (EcACP) shuttles substrates to a series of partner enzymes. Here we present a method by which EcACP is labeled with a solvatochromic dye, 4-DMN, and then allowed to interact with its various partner enzymes. Upon interaction, there is a large increase in fluorescence intensity which is easily monitored via fluorometer or plate reader. This method is useful in the study of known PPI, hypothetical PPI and in evaluation of inhibitors of both partner enzyme active site and of the PPI itself.
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Affiliation(s)
- Katherine Charov
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States.
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Davis TD, Michaud JM, Burkart MD. Active site labeling of fatty acid and polyketide acyl-carrier protein transacylases. Org Biomol Chem 2020; 17:4720-4724. [PMID: 31044196 DOI: 10.1039/c8ob03229g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metabolic engineering of fatty acids and polyketides remains challenging due to unresolved protein-protein interactions that are essential to synthase activity. While several chemical probes have been developed to capture and visualize protein interfaces in these systems, acyl carrier protein (ACP) transacylase (AT) domains remain elusive. Herein, we combine a mutational strategy with fluorescent probe design to expedite the study of AT domains from fatty acid and polyketide synthases. We describe the design and evaluation of inhibitor-inspired and substrate-mimetic reporters containing sulfonyl fluoride and β-lactone warheads. Moreover, specific active-site labeling occurs by optimizing pH, time, and probe concentration, and selective labeling is achieved in the presence of inhibitors of competing domains. These findings provide a panel of AT-targeting probes and set the stage for future combinatorial biosynthetic and drug discovery initiatives.
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Affiliation(s)
- Tony D Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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Acheampong KK, Kokona B, Braun GA, Jacobsen DR, Johnson KA, Charkoudian LK. Colorimetric Assay Reports on Acyl Carrier Protein Interactions. Sci Rep 2019; 9:15589. [PMID: 31666546 PMCID: PMC6821831 DOI: 10.1038/s41598-019-51554-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 09/25/2019] [Indexed: 01/15/2023] Open
Abstract
The ability to produce new molecules of potential pharmaceutical relevance via combinatorial biosynthesis hinges on improving our understanding of acyl-carrier protein (ACP)-protein interactions. However, the weak and transient nature of these interactions makes them difficult to study using traditional spectroscopic approaches. Herein we report that converting the terminal thiol of the E. coli ACP 4'-phosphopantetheine arm into a mixed disulfide with 2-nitro-5-thiobenzoate ion (TNB-) activates this site to form a selective covalent cross-link with the active site cysteine of a cognate ketoacyl synthase (KS). The concomitant release of TNB2-, which absorbs at 412 nm, provides a visual and quantitative measure of mechanistically relevant ACP-KS interactions. The colorimetric assay can propel the engineering of biosynthetic routes to novel chemical diversity by providing a high-throughput screen for functional hybrid ACP-KS partnerships as well as the discovery of novel antimicrobial agents by enabling the rapid identification of small molecule inhibitors of ACP-KS interactions.
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Affiliation(s)
- Kofi K Acheampong
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | - Gabriel A Braun
- Department of Chemistry, Haverford College, Haverford, PA, 19041-1391, USA
| | | | - Karl A Johnson
- Department of Biology, Haverford College, Haverford, PA, 19041-1391, USA.
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Charov K, Burkart MD. A Single Tool to Monitor Multiple Protein-Protein Interactions of the Escherichia coli Acyl Carrier Protein. ACS Infect Dis 2019; 5:1518-1523. [PMID: 31317739 DOI: 10.1021/acsinfecdis.9b00150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein-protein interactions are ubiquitous to all domains of life and have gained recent interest as drug targets. However, many current methods to study protein-protein interactions can be costly and are low-throughput. Here, we demonstrate a solvatochromic tool based on the natural post-translational modification of the Escherichia coli acyl carrier protein (EcACP) used to visualize protein-protein interactions between EcACP and 13 different partner enzymes from several biosynthetic pathways. We use this tool to confirm proposed interactions between EcACP and both catalytic and regulatory proteins. We also show the utility of this method toward detecting allosteric changes to partner enzyme structure and the validation of active site inhibitors. We anticipate the future adaptation of this assay into a high-throughput screen for antibiotic discovery.
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Affiliation(s)
- Katherine Charov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
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